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Volume 26, Number 8—August 2020
Synopsis

US CDC Real-Time Reverse Transcription PCR Panel for Detection of Severe Acute Respiratory Syndrome Coronavirus 2

Xiaoyan Lu, Lijuan Wang, Senthilkumar K. Sakthivel, Brett Whitaker, Janna Murray, Shifaq Kamili, Brian Lynch, Lakshmi Malapati, Stephen A. Burke, Jennifer Harcourt, Azaibi Tamin, Natalie J. Thornburg, Julie M. Villanueva, and Stephen LindstromComments to Author 
Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (X. Lu, B. Whitaker, S.A. Burke, J. Harcourt, A. Tamin, N.J. Thornburg, J.M. Villanueva, S. Lindstrom); Synergy America, Inc., Atlanta (L. Wang, S. Kamili); Eagle Contracting, Atlanta (S.K. Sakthivel, J. Murray, B. Lynch); Leidos, Atlanta (L. Malapati); Battelle, Atlanta (S.A. Burke)

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Table 1

Assay primer/probe sequences for the US CDC rRT-PCR panel for detection of SARS-CoV-2*

Assay Genome target Genome location Primers and probes† Sequence, 5′→3′ Amplicon size, bp Assay use
N1
Nucleocapsid gene
28303–28322‡ Forward primer GACCCCAAAATCAGCGAAAT 73
SARS-CoV-2
28374–28351‡ Reverse primer TCTGGTTACTGCCAGTTGAATCTG
28325–28348‡
Probe
ACCCCGCATTACGTTTGGTGGACC
N2
Nucleocapsid gene
29180–29199‡ Forward primer TTACAAACATTGGCCGCAAA 67
SARS-CoV-2
29246–29228‡ Reverse primer GCGCGACATTCCGAAGAA
29204–29226‡
Probe
ACAATTTGCCCCCAGCGCTTCAG
N3
Nucleocapsid gene
28697–28718‡ Forward primer GGGAGCCTTGAATACACCAAAA 72
SARS-CoV-2,
SARS-CoV, and other Sarbecoviruses§
28768–28748‡ Reverse primer TGTAGCACGATTGCAGCATTG
28720–28743‡
Probe
AYCACATTGGCACCCGCAATCCTG
RP¶ Human RNase P gene 50–68# Forward primer AGATTTGGACCTGCGAGCG 65 Sample quality control
114–95# Reverse primer GAGCGGCTGTCTCCACAAGT
71–93# Probe TTCTGACCTGAAGGCTCTGCGCG

*CDC, Centers for Disease Control and Prevention; N, nucleocapsid protein gene; RP, ribonuclease P gene; rRT-PCR, real-time reverse transcription PCR; SARS-CoV-2, severe acute respiratory coronavirus 2.
†Probes labeled at the 5′-end with the reporter molecule 6-carboxyfluorescein (FAM) and at the 3′-end with Black Hole Quencher 1 (Biosearch Technologies Inc., https://www.biosearchtech.com).
‡Nucleotide numbering based on SARS-CoV-2 (accession no. MN908947).
§Bat- and civet-SARS–like coronaviruses.
¶Primer/probe sequences from (10).
#Nucleotide numbering based on human RP mRNA (accession no. NM_006413).

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Page updated: July 17, 2020
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